310 research outputs found
Monte Carlo Update for Chain Molecules: Biased Gaussian Steps in Torsional Space
We develop a new elementary move for simulations of polymer chains in torsion
angle space. The method is flexible and easy to implement. Tentative updates
are drawn from a (conformation-dependent) Gaussian distribution that favors
approximately local deformations of the chain. The degree of bias is controlled
by a parameter b. The method is tested on a reduced model protein with 54 amino
acids and the Ramachandran torsion angles as its only degrees of freedom, for
different b. Without excessive fine tuning, we find that the effective step
size can be increased by a factor of three compared to the unbiased b=0 case.
The method may be useful for kinetic studies, too.Comment: 14 pages, 4 figure
Requirements for contractility in disordered cytoskeletal bundles
Actomyosin contractility is essential for biological force generation, and is
well understood in highly organized structures such as striated muscle.
Additionally, actomyosin bundles devoid of this organization are known to
contract both in vivo and in vitro, which cannot be described by standard
muscle models. To narrow down the search for possible contraction mechanisms in
these systems, we investigate their microscopic symmetries. We show that
contractile behavior requires non-identical motors that generate large enough
forces to probe the nonlinear elastic behavior of F-actin. This suggests a role
for filament buckling in the contraction of these bundles, consistent with
recent experimental results on reconstituted actomyosin bundles.Comment: 10 pages, 6 figures; text shortene
Contractile units in disordered actomyosin bundles arise from F-actin buckling
Bundles of filaments and motors are central to contractility in cells. The
classic example is striated muscle, where actomyosin contractility is mediated
by highly organized sarcomeres which act as fundamental contractile units.
However, many contractile bundles in vivo and in vitro lack sarcomeric
organization. Here we propose a model for how contractility can arise in
actomyosin bundles without sarcomeric organization and validate its predictions
with experiments on a reconstituted system. In the model, internal stresses in
frustrated arrangements of motors with diverse velocities cause filaments to
buckle, leading to overall shortening. We describe the onset of buckling in the
presence of stochastic actin-myosin detachment and predict that
buckling-induced contraction occurs in an intermediate range of motor
densities. We then calculate the size of the "contractile units" associated
with this process. Consistent with these results, our reconstituted actomyosin
bundles contract at relatively high motor density, and we observe buckling at
the predicted length scale.Comment: 5 pages, 4 figures, Supporting text and movies attache
Depairing critical current achieved in superconducting thin films with through-thickness arrays of artificial pinning centers
Large area arrays of through-thickness nanoscale pores have been milled into
superconducting Nb thin films via a process utilizing anodized aluminum oxide
thin film templates. These pores act as artificial flux pinning centers,
increasing the superconducting critical current, Jc, of the Nb films. By
optimizing the process conditions including anodization time, pore size and
milling time, Jc values approaching and in some cases matching the
Ginzburg-Landau depairing current of 30 MA/cm^2 at 5 K have been achieved - a
Jc enhancement over as-deposited films of more than 50 times. In the field
dependence of Jc, a matching field corresponding to the areal pore density has
also been clearly observed. The effect of back-filling the pores with magnetic
material has then been investigated. While back-filling with Co has been
successfully achieved, the effect of the magnetic material on Jc has been found
to be largely detrimental compared to voids, although a distinct influence of
the magnetic material in producing a hysteretic Jc versus applied field
behavior has been observed. This behavior has been tested for compatibility
with currently proposed models of magnetic pinning and found to be most closely
explained by a model describing the magnetic attraction between the flux
vortices and the magnetic inclusions.Comment: 9 pages, 10 figure
Structural Responses of Quasi-2D Colloid Fluids to Excitations Elicited by Nonequilibrium Perturbations
We investigate the response of a dense monodisperse quasi-two-dimensional
(q2D) colloid suspension when a particle is dragged by a constant velocity
optical trap. Consistent with microrheological studies of other geometries, the
perturbation induces a leading density wave and trailing wake, and we use
Stokesian Dynamics (SD) simulations to parse direct colloid-colloid and
hydrodynamic interactions. We go on to analyze the underlying individual
particle-particle collisions in the experimental images. The displacements of
particles form chains reminiscent of stress propagation in sheared granular
materials. From these data, we can reconstruct steady-state dipolar flow
patterns that were predicted for dilute suspensions and previously observed in
granular analogs to our system. The decay of this field differs, however, from
point Stokeslet calculations, indicating that the finite size of the colloids
is important. Moreover, there is a pronounced angular dependence that
corresponds to the surrounding colloid structure, which evolves in response to
the perturbation. Put together, our results show that the response of the
complex fluid is highly anisotropic owing to the fact that the effects of the
perturbation propagate through the structured medium via chains of
colloid-colloid collisions
Exact Solution of the Munoz-Eaton Model for Protein Folding
A transfer-matrix formalism is introduced to evaluate exactly the partition
function of the Munoz-Eaton model, relating the folding kinetics of proteins of
known structure to their thermodynamics and topology. This technique can be
used for a generic protein, for any choice of the energy and entropy
parameters, and in principle allows the model to be used as a first tool to
characterize the dynamics of a protein of known native state and equilibrium
population. Applications to a -hairpin and to protein CI-2, with
comparisons to previous results, are also shown.Comment: 4 pages, 5 figures, RevTeX 4. To be published in Phys. Rev. Let
Optimization of drift gases for accuracy in pressurized drift tubes
Modern detectors such as ATLAS use pressurized drift tubes to minimize diffusion and achieve high coordinate accuracy. However, the coordinate accuracy depends on the exact knowledge of converting measured times into coordinates. Linear space-time relationships are best for reconstruction, but difficult to achieve in the field. Previous mixtures, which contained methane or other organic quenchers, are disfavored because of ageing problems. From our studies of nitrogen and carbon dioxide, two mixtures with only small deviations from linearity were determined and measured. Scaling laws for different pressures and magnetic fields are also given
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